Starting phenix.real_space_refine on Mon Jul 6 05:42:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ozf_17307/07_2026/8ozf_17307.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ozf_17307/07_2026/8ozf_17307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ozf_17307/07_2026/8ozf_17307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ozf_17307/07_2026/8ozf_17307.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ozf_17307/07_2026/8ozf_17307.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ozf_17307/07_2026/8ozf_17307.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ozf_17307/07_2026/8ozf_17307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ozf_17307/07_2026/8ozf_17307.map" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1220 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 136 5.49 5 S 96 5.16 5 C 20266 2.51 5 N 5310 2.21 5 O 6268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 122 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32076 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "B" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "C" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "E" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "F" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "G" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "H" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "I" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "J" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "K" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "L" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "M" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "N" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "O" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "P" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "Q" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.31, per 1000 atoms: 0.23 Number of scatterers: 32076 At special positions: 0 Unit cell: (177.87, 206.91, 169.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 136 15.00 O 6268 8.00 N 5310 7.00 C 20266 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 1.3 seconds 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6792 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 32 sheets defined 40.2% alpha, 13.9% beta 22 base pairs and 95 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'A' and resid 14 through 29 removed outlier: 3.508A pdb=" N GLY A 27 " --> pdb=" O LEU A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.905A pdb=" N GLU A 50 " --> pdb=" O TRP A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 70 removed outlier: 4.477A pdb=" N GLN A 70 " --> pdb=" O SER A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 89 Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.722A pdb=" N ILE A 108 " --> pdb=" O TYR A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 138 Processing helix chain 'A' and resid 146 through 157 removed outlier: 3.914A pdb=" N SER A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 219 through 224 removed outlier: 3.510A pdb=" N ASP A 222 " --> pdb=" O TRP A 219 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE A 223 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR A 224 " --> pdb=" O TYR A 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 219 through 224' Processing helix chain 'A' and resid 227 through 233 removed outlier: 4.000A pdb=" N THR A 232 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.596A pdb=" N THR A 238 " --> pdb=" O LYS A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 257 through 280 removed outlier: 3.702A pdb=" N ARG A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE A 265 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN A 267 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 353 through 366 Processing helix chain 'A' and resid 369 through 384 removed outlier: 4.319A pdb=" N THR A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS A 376 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 22 through 31 Processing helix chain 'B' and resid 46 through 62 removed outlier: 3.584A pdb=" N LYS B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 82 Processing helix chain 'B' and resid 97 through 106 removed outlier: 3.835A pdb=" N PHE B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR B 106 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 132 removed outlier: 3.607A pdb=" N PHE B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 150 removed outlier: 3.675A pdb=" N TYR B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'B' and resid 205 through 214 removed outlier: 3.761A pdb=" N LEU B 214 " --> pdb=" O PHE B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 218 Processing helix chain 'B' and resid 230 through 234 Processing helix chain 'B' and resid 248 through 265 removed outlier: 3.676A pdb=" N ALA B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 351 removed outlier: 4.369A pdb=" N GLN B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 377 removed outlier: 3.555A pdb=" N VAL B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 463 removed outlier: 3.973A pdb=" N LEU B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 491 removed outlier: 3.733A pdb=" N ARG B 481 " --> pdb=" O PRO B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'C' and resid 10 through 28 removed outlier: 3.734A pdb=" N ASN C 15 " --> pdb=" O THR C 11 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ASP C 16 " --> pdb=" O PRO C 12 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N PHE C 17 " --> pdb=" O ASP C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 56 Processing helix chain 'C' and resid 65 through 70 removed outlier: 4.335A pdb=" N GLN C 70 " --> pdb=" O SER C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 89 Processing helix chain 'C' and resid 109 through 115 removed outlier: 3.671A pdb=" N LEU C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 139 removed outlier: 3.899A pdb=" N GLY C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C 128 " --> pdb=" O TRP C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 158 Processing helix chain 'C' and resid 190 through 194 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 227 through 231 Processing helix chain 'C' and resid 234 through 238 removed outlier: 3.597A pdb=" N THR C 238 " --> pdb=" O LYS C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 257 through 280 removed outlier: 3.518A pdb=" N LYS C 262 " --> pdb=" O ASN C 258 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE C 265 " --> pdb=" O CYS C 261 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL C 266 " --> pdb=" O LYS C 262 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN C 267 " --> pdb=" O ARG C 263 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 366 Processing helix chain 'C' and resid 369 through 385 removed outlier: 3.848A pdb=" N THR C 375 " --> pdb=" O ASN C 371 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LYS C 376 " --> pdb=" O THR C 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 17 No H-bonds generated for 'chain 'E' and resid 15 through 17' Processing helix chain 'E' and resid 22 through 31 Processing helix chain 'E' and resid 46 through 62 removed outlier: 3.608A pdb=" N LYS E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE E 52 " --> pdb=" O GLN E 48 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS E 62 " --> pdb=" O ASP E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 82 Processing helix chain 'E' and resid 99 through 104 removed outlier: 3.921A pdb=" N PHE E 104 " --> pdb=" O ASP E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 132 removed outlier: 3.763A pdb=" N LYS E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU E 132 " --> pdb=" O ALA E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 151 removed outlier: 3.705A pdb=" N TYR E 148 " --> pdb=" O PRO E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 214 Processing helix chain 'E' and resid 230 through 234 removed outlier: 3.575A pdb=" N ASP E 233 " --> pdb=" O ALA E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 264 Processing helix chain 'E' and resid 331 through 351 removed outlier: 3.637A pdb=" N TYR E 346 " --> pdb=" O SER E 342 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN E 349 " --> pdb=" O SER E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 377 removed outlier: 3.706A pdb=" N TRP E 370 " --> pdb=" O ASN E 366 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL E 376 " --> pdb=" O ALA E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 430 Processing helix chain 'E' and resid 451 through 463 removed outlier: 3.739A pdb=" N LEU E 460 " --> pdb=" O LEU E 456 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER E 461 " --> pdb=" O LYS E 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 491 removed outlier: 3.766A pdb=" N ASP E 484 " --> pdb=" O LEU E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 506 removed outlier: 3.710A pdb=" N TYR E 505 " --> pdb=" O ALA E 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 29 Processing helix chain 'F' and resid 43 through 56 removed outlier: 4.611A pdb=" N SER F 47 " --> pdb=" O VAL F 43 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU F 50 " --> pdb=" O TRP F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 70 removed outlier: 3.744A pdb=" N GLN F 70 " --> pdb=" O TYR F 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 67 through 70' Processing helix chain 'F' and resid 71 through 89 Processing helix chain 'F' and resid 104 through 108 removed outlier: 4.023A pdb=" N ILE F 108 " --> pdb=" O TYR F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 114 removed outlier: 4.693A pdb=" N ARG F 114 " --> pdb=" O ILE F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 138 Processing helix chain 'F' and resid 146 through 158 removed outlier: 3.967A pdb=" N SER F 150 " --> pdb=" O ASP F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 194 Processing helix chain 'F' and resid 199 through 203 removed outlier: 3.803A pdb=" N GLU F 202 " --> pdb=" O ASP F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 233 removed outlier: 3.716A pdb=" N GLU F 231 " --> pdb=" O PRO F 228 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR F 232 " --> pdb=" O LYS F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 238 removed outlier: 3.654A pdb=" N THR F 238 " --> pdb=" O LYS F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 249 removed outlier: 3.502A pdb=" N ILE F 246 " --> pdb=" O PRO F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 262 Processing helix chain 'F' and resid 262 through 280 removed outlier: 3.521A pdb=" N VAL F 266 " --> pdb=" O LYS F 262 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN F 267 " --> pdb=" O ARG F 263 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU F 268 " --> pdb=" O LEU F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 302 No H-bonds generated for 'chain 'F' and resid 300 through 302' Processing helix chain 'F' and resid 353 through 366 Processing helix chain 'F' and resid 369 through 384 removed outlier: 3.747A pdb=" N THR F 375 " --> pdb=" O ASN F 371 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS F 376 " --> pdb=" O THR F 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 23 through 31 Processing helix chain 'G' and resid 46 through 62 removed outlier: 3.932A pdb=" N LYS G 51 " --> pdb=" O LYS G 47 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE G 52 " --> pdb=" O GLN G 48 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE G 53 " --> pdb=" O GLY G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 83 Processing helix chain 'G' and resid 97 through 106 removed outlier: 3.793A pdb=" N PHE G 104 " --> pdb=" O ASP G 100 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR G 106 " --> pdb=" O GLY G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 132 Processing helix chain 'G' and resid 145 through 150 Processing helix chain 'G' and resid 158 through 162 removed outlier: 3.579A pdb=" N MET G 161 " --> pdb=" O PRO G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 214 removed outlier: 3.649A pdb=" N LEU G 214 " --> pdb=" O PHE G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 218 Processing helix chain 'G' and resid 230 through 234 Processing helix chain 'G' and resid 248 through 264 removed outlier: 3.781A pdb=" N ALA G 259 " --> pdb=" O THR G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 331 through 351 removed outlier: 3.695A pdb=" N TYR G 346 " --> pdb=" O SER G 342 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLN G 349 " --> pdb=" O SER G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 366 through 377 removed outlier: 3.732A pdb=" N TRP G 370 " --> pdb=" O ASN G 366 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA G 372 " --> pdb=" O GLN G 368 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL G 376 " --> pdb=" O ALA G 372 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR G 377 " --> pdb=" O PHE G 373 " (cutoff:3.500A) Processing helix chain 'G' and resid 451 through 463 removed outlier: 3.818A pdb=" N SER G 461 " --> pdb=" O LYS G 457 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 491 Processing helix chain 'G' and resid 502 through 506 Processing helix chain 'H' and resid 14 through 28 Processing helix chain 'H' and resid 34 through 39 removed outlier: 3.573A pdb=" N LEU H 39 " --> pdb=" O ASP H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 56 Processing helix chain 'H' and resid 71 through 89 Processing helix chain 'H' and resid 109 through 114 Processing helix chain 'H' and resid 123 through 138 removed outlier: 3.650A pdb=" N GLY H 127 " --> pdb=" O SER H 123 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU H 128 " --> pdb=" O TRP H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 158 removed outlier: 3.709A pdb=" N PHE H 158 " --> pdb=" O TYR H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 194 Processing helix chain 'H' and resid 227 through 233 removed outlier: 3.575A pdb=" N THR H 232 " --> pdb=" O LYS H 229 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR H 233 " --> pdb=" O THR H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 234 through 238 Processing helix chain 'H' and resid 243 through 249 Processing helix chain 'H' and resid 257 through 281 removed outlier: 3.722A pdb=" N ARG H 263 " --> pdb=" O ALA H 259 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE H 265 " --> pdb=" O CYS H 261 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN H 267 " --> pdb=" O ARG H 263 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU H 268 " --> pdb=" O LEU H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 300 through 304 removed outlier: 3.555A pdb=" N LYS H 304 " --> pdb=" O GLU H 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 353 through 366 Processing helix chain 'H' and resid 369 through 385 removed outlier: 4.160A pdb=" N THR H 375 " --> pdb=" O ASN H 371 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS H 376 " --> pdb=" O THR H 372 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 17 No H-bonds generated for 'chain 'M' and resid 15 through 17' Processing helix chain 'M' and resid 23 through 31 Processing helix chain 'M' and resid 46 through 62 removed outlier: 4.117A pdb=" N ILE M 52 " --> pdb=" O GLN M 48 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 83 Processing helix chain 'M' and resid 97 through 106 removed outlier: 3.666A pdb=" N PHE M 104 " --> pdb=" O ASP M 100 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 131 removed outlier: 3.649A pdb=" N LYS M 124 " --> pdb=" O LEU M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 150 removed outlier: 3.542A pdb=" N TYR M 148 " --> pdb=" O PRO M 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 162 Processing helix chain 'M' and resid 205 through 214 removed outlier: 3.610A pdb=" N LEU M 214 " --> pdb=" O PHE M 210 " (cutoff:3.500A) Processing helix chain 'M' and resid 215 through 218 removed outlier: 3.502A pdb=" N THR M 218 " --> pdb=" O LEU M 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 215 through 218' Processing helix chain 'M' and resid 230 through 234 Processing helix chain 'M' and resid 248 through 264 Processing helix chain 'M' and resid 331 through 351 removed outlier: 4.963A pdb=" N GLN M 349 " --> pdb=" O SER M 345 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 377 removed outlier: 3.613A pdb=" N TRP M 370 " --> pdb=" O ASN M 366 " (cutoff:3.500A) Processing helix chain 'M' and resid 426 through 430 Processing helix chain 'M' and resid 451 through 463 removed outlier: 3.809A pdb=" N LEU M 460 " --> pdb=" O LEU M 456 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER M 461 " --> pdb=" O LYS M 457 " (cutoff:3.500A) Processing helix chain 'M' and resid 477 through 491 Processing helix chain 'M' and resid 502 through 506 removed outlier: 3.521A pdb=" N TYR M 505 " --> pdb=" O ALA M 502 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 33 removed outlier: 6.062A pdb=" N ILE A 5 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LYS A 4 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N LEU A 61 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N PHE A 6 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N VAL A 63 " --> pdb=" O PHE A 6 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N SER A 8 " --> pdb=" O VAL A 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 178 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 169 through 178 current: chain 'A' and resid 291 through 294 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 291 through 294 current: chain 'A' and resid 317 through 328 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 334 through 344 current: chain 'A' and resid 400 through 412 removed outlier: 4.164A pdb=" N LYS B 2 " --> pdb=" O LYS A 409 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 210 Processing sheet with id=AA4, first strand: chain 'A' and resid 304 through 305 removed outlier: 3.668A pdb=" N PHE A 305 " --> pdb=" O THR A 308 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 5 through 6 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 5 through 6 current: chain 'B' and resid 297 through 301 removed outlier: 7.702A pdb=" N CYS B 298 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLY B 318 " --> pdb=" O CYS B 298 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA B 300 " --> pdb=" O GLU B 316 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 315 through 320 current: chain 'B' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 382 through 389 current: chain 'B' and resid 417 through 420 Processing sheet with id=AA6, first strand: chain 'B' and resid 19 through 20 Processing sheet with id=AA7, first strand: chain 'B' and resid 92 through 95 removed outlier: 6.596A pdb=" N GLY B 42 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE B 142 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE B 44 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TRP B 139 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N PHE B 224 " --> pdb=" O TRP B 139 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N VAL B 141 " --> pdb=" O PHE B 224 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 32 through 33 removed outlier: 5.852A pdb=" N ILE C 5 " --> pdb=" O TRP C 33 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS C 4 " --> pdb=" O LYS C 59 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N LEU C 61 " --> pdb=" O LYS C 4 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE C 6 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL C 63 " --> pdb=" O PHE C 6 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N SER C 8 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C 62 " --> pdb=" O ILE C 95 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 3 removed outlier: 4.218A pdb=" N LYS E 2 " --> pdb=" O LYS C 409 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 175 through 180 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 175 through 180 current: chain 'C' and resid 292 through 294 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 292 through 294 current: chain 'C' and resid 317 through 328 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 334 through 344 current: chain 'C' and resid 400 through 404 Processing sheet with id=AB2, first strand: chain 'C' and resid 208 through 210 Processing sheet with id=AB3, first strand: chain 'C' and resid 304 through 305 Processing sheet with id=AB4, first strand: chain 'E' and resid 5 through 6 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 5 through 6 current: chain 'E' and resid 297 through 305 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 311 through 315 current: chain 'E' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 382 through 389 current: chain 'E' and resid 417 through 420 Processing sheet with id=AB5, first strand: chain 'E' and resid 19 through 20 Processing sheet with id=AB6, first strand: chain 'E' and resid 92 through 95 removed outlier: 6.191A pdb=" N GLY E 42 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE E 142 " --> pdb=" O GLY E 42 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE E 44 " --> pdb=" O ILE E 142 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 425 through 426 removed outlier: 3.912A pdb=" N VAL E 426 " --> pdb=" O THR E 431 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR E 431 " --> pdb=" O VAL E 426 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 32 through 33 removed outlier: 6.337A pdb=" N ILE F 5 " --> pdb=" O TRP F 33 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LYS F 4 " --> pdb=" O THR F 57 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS F 59 " --> pdb=" O LYS F 4 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU F 62 " --> pdb=" O ILE F 95 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ILE F 118 " --> pdb=" O ILE F 94 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 165 through 180 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 165 through 180 current: chain 'F' and resid 291 through 294 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 291 through 294 current: chain 'F' and resid 317 through 328 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 334 through 344 current: chain 'F' and resid 400 through 415 removed outlier: 3.621A pdb=" N LYS G 2 " --> pdb=" O LYS F 409 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASN F 413 " --> pdb=" O LEU G 4 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N TYR G 6 " --> pdb=" O ASN F 413 " (cutoff:3.500A) removed outlier: 10.337A pdb=" N SER F 415 " --> pdb=" O TYR G 6 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 2 through 6 current: chain 'G' and resid 356 through 361 removed outlier: 6.391A pdb=" N VAL G 357 " --> pdb=" O VAL G 384 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N VAL G 386 " --> pdb=" O VAL G 357 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE G 359 " --> pdb=" O VAL G 386 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ILE G 388 " --> pdb=" O ILE G 359 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA G 361 " --> pdb=" O ILE G 388 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 382 through 389 current: chain 'G' and resid 417 through 420 Processing sheet with id=AC1, first strand: chain 'F' and resid 186 through 188 Processing sheet with id=AC2, first strand: chain 'F' and resid 304 through 305 Processing sheet with id=AC3, first strand: chain 'G' and resid 19 through 20 Processing sheet with id=AC4, first strand: chain 'G' and resid 92 through 95 removed outlier: 6.483A pdb=" N GLY G 42 " --> pdb=" O PHE G 140 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE G 142 " --> pdb=" O GLY G 42 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE G 44 " --> pdb=" O ILE G 142 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 282 through 286 Processing sheet with id=AC6, first strand: chain 'H' and resid 32 through 33 removed outlier: 5.861A pdb=" N ILE H 5 " --> pdb=" O TRP H 33 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LYS H 4 " --> pdb=" O LYS H 59 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N LEU H 61 " --> pdb=" O LYS H 4 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N PHE H 6 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL H 63 " --> pdb=" O PHE H 6 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N SER H 8 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ILE H 118 " --> pdb=" O ILE H 94 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 2 through 3 removed outlier: 5.508A pdb=" N LYS H 167 " --> pdb=" O VAL H 414 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 175 through 177 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 175 through 177 current: chain 'H' and resid 291 through 294 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 291 through 294 current: chain 'H' and resid 317 through 328 Processing sheet with id=AC9, first strand: chain 'H' and resid 208 through 210 removed outlier: 3.628A pdb=" N LEU H 185 " --> pdb=" O ILE H 241 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 390 through 394 Processing sheet with id=AD2, first strand: chain 'M' and resid 5 through 6 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 5 through 6 current: chain 'M' and resid 297 through 301 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 315 through 316 current: chain 'M' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 382 through 389 current: chain 'M' and resid 417 through 420 Processing sheet with id=AD3, first strand: chain 'M' and resid 19 through 20 Processing sheet with id=AD4, first strand: chain 'M' and resid 92 through 95 removed outlier: 6.336A pdb=" N GLY M 42 " --> pdb=" O PHE M 140 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ILE M 142 " --> pdb=" O GLY M 42 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE M 44 " --> pdb=" O ILE M 142 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TRP M 139 " --> pdb=" O GLN M 222 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N PHE M 224 " --> pdb=" O TRP M 139 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL M 141 " --> pdb=" O PHE M 224 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 304 through 305 1035 hydrogen bonds defined for protein. 2820 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 95 stacking parallelities Total time for adding SS restraints: 7.38 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8567 1.33 - 1.46: 7187 1.46 - 1.58: 16964 1.58 - 1.70: 276 1.70 - 1.82: 148 Bond restraints: 33142 Sorted by residual: bond pdb=" C2' AR6 H 501 " pdb=" C3' AR6 H 501 " ideal model delta sigma weight residual 1.532 1.235 0.297 2.00e-02 2.50e+03 2.20e+02 bond pdb=" C2' AR6 A 501 " pdb=" C3' AR6 A 501 " ideal model delta sigma weight residual 1.532 1.240 0.292 2.00e-02 2.50e+03 2.13e+02 bond pdb=" C3D AR6 A 501 " pdb=" C4D AR6 A 501 " ideal model delta sigma weight residual 1.529 1.254 0.275 2.00e-02 2.50e+03 1.89e+02 bond pdb=" C3D AR6 H 501 " pdb=" C4D AR6 H 501 " ideal model delta sigma weight residual 1.529 1.259 0.270 2.00e-02 2.50e+03 1.82e+02 bond pdb=" C1D AR6 H 501 " pdb=" C2D AR6 H 501 " ideal model delta sigma weight residual 1.529 1.287 0.242 2.00e-02 2.50e+03 1.46e+02 ... (remaining 33137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 45089 3.44 - 6.88: 262 6.88 - 10.32: 15 10.32 - 13.76: 6 13.76 - 17.20: 4 Bond angle restraints: 45376 Sorted by residual: angle pdb=" C LEU A 39 " pdb=" N ASP A 40 " pdb=" CA ASP A 40 " ideal model delta sigma weight residual 121.54 133.61 -12.07 1.91e+00 2.74e-01 3.99e+01 angle pdb=" O3A AR6 A 501 " pdb=" PA AR6 A 501 " pdb=" O5' AR6 A 501 " ideal model delta sigma weight residual 93.19 110.39 -17.20 3.00e+00 1.11e-01 3.29e+01 angle pdb=" C LEU F 39 " pdb=" N ASP F 40 " pdb=" CA ASP F 40 " ideal model delta sigma weight residual 121.54 132.26 -10.72 1.91e+00 2.74e-01 3.15e+01 angle pdb=" C GLU M 352 " pdb=" N TYR M 353 " pdb=" CA TYR M 353 " ideal model delta sigma weight residual 120.49 128.24 -7.75 1.42e+00 4.96e-01 2.98e+01 angle pdb=" C ALA H 145 " pdb=" CA ALA H 145 " pdb=" CB ALA H 145 " ideal model delta sigma weight residual 116.63 110.40 6.23 1.16e+00 7.43e-01 2.88e+01 ... (remaining 45371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.52: 18969 32.52 - 65.03: 629 65.03 - 97.55: 45 97.55 - 130.07: 5 130.07 - 162.58: 12 Dihedral angle restraints: 19660 sinusoidal: 9152 harmonic: 10508 Sorted by residual: dihedral pdb=" O4' U N 9 " pdb=" C1' U N 9 " pdb=" N1 U N 9 " pdb=" C2 U N 9 " ideal model delta sinusoidal sigma weight residual 200.00 37.42 162.58 1 1.50e+01 4.44e-03 8.34e+01 dihedral pdb=" O4' U I 9 " pdb=" C1' U I 9 " pdb=" N1 U I 9 " pdb=" C2 U I 9 " ideal model delta sinusoidal sigma weight residual 200.00 40.57 159.43 1 1.50e+01 4.44e-03 8.26e+01 dihedral pdb=" O4' U O 13 " pdb=" C1' U O 13 " pdb=" N1 U O 13 " pdb=" C2 U O 13 " ideal model delta sinusoidal sigma weight residual 200.00 41.01 158.99 1 1.50e+01 4.44e-03 8.25e+01 ... (remaining 19657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 4343 0.064 - 0.128: 605 0.128 - 0.192: 28 0.192 - 0.256: 5 0.256 - 0.321: 3 Chirality restraints: 4984 Sorted by residual: chirality pdb=" C3' AR6 H 501 " pdb=" C2' AR6 H 501 " pdb=" C4' AR6 H 501 " pdb=" O3' AR6 H 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.39 -0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" C3' AR6 A 501 " pdb=" C2' AR6 A 501 " pdb=" C4' AR6 A 501 " pdb=" O3' AR6 A 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.40 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CB ILE C 7 " pdb=" CA ILE C 7 " pdb=" CG1 ILE C 7 " pdb=" CG2 ILE C 7 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 4981 not shown) Planarity restraints: 5238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 194 " -0.070 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO C 195 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO C 195 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 195 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 143 " -0.048 5.00e-02 4.00e+02 7.34e-02 8.61e+00 pdb=" N PRO G 144 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO G 144 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO G 144 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 86 " -0.020 2.00e-02 2.50e+03 1.77e-02 7.80e+00 pdb=" CG TRP M 86 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP M 86 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP M 86 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP M 86 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP M 86 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP M 86 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 86 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 86 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP M 86 " -0.005 2.00e-02 2.50e+03 ... (remaining 5235 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 824 2.67 - 3.23: 31292 3.23 - 3.78: 52937 3.78 - 4.34: 72595 4.34 - 4.90: 112544 Nonbonded interactions: 270192 Sorted by model distance: nonbonded pdb=" OG SER M 493 " pdb=" OD1 ASP M 495 " model vdw 2.112 3.040 nonbonded pdb=" OG SER F 404 " pdb=" OE1 GLU F 406 " model vdw 2.135 3.040 nonbonded pdb=" OG1 THR G 387 " pdb=" OD1 ASN G 446 " model vdw 2.136 3.040 nonbonded pdb=" OH TYR F 416 " pdb=" O THR G 404 " model vdw 2.151 3.040 nonbonded pdb=" OG1 THR G 363 " pdb=" OP1 DA P 8 " model vdw 2.168 3.040 ... (remaining 270187 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 418) selection = chain 'C' selection = chain 'F' selection = (chain 'H' and resid 1 through 418) } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'G' selection = chain 'M' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'P' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 34.050 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.297 33142 Z= 0.323 Angle : 0.759 17.195 45376 Z= 0.440 Chirality : 0.043 0.321 4984 Planarity : 0.005 0.104 5238 Dihedral : 16.009 162.584 12868 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.87 % Favored : 94.76 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.14), residues: 3532 helix: 0.59 (0.16), residues: 1156 sheet: -0.62 (0.21), residues: 558 loop : -1.29 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 114 TYR 0.021 0.001 TYR C 293 PHE 0.046 0.002 PHE C 273 TRP 0.046 0.002 TRP M 86 HIS 0.009 0.001 HIS G 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.32 (33142) covalent geometry : angle 0.75901 / 0.44 (45376) hydrogen bonds : bond 0.19829 / 13.41 ( 1079) hydrogen bonds : angle 7.84857 / 5.55 ( 2908) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8689 (mtp-110) cc_final: 0.8320 (mtp-110) REVERT: A 383 TYR cc_start: 0.7564 (t80) cc_final: 0.7142 (t80) REVERT: A 393 LEU cc_start: 0.7424 (mt) cc_final: 0.7121 (mt) REVERT: B 258 THR cc_start: 0.8339 (m) cc_final: 0.8001 (m) REVERT: B 397 TYR cc_start: 0.8384 (m-80) cc_final: 0.7902 (m-80) REVERT: C 89 LYS cc_start: 0.7667 (mmtm) cc_final: 0.7004 (pttm) REVERT: C 193 MET cc_start: 0.4425 (mtm) cc_final: 0.3460 (mtm) REVERT: C 217 PHE cc_start: 0.7428 (m-80) cc_final: 0.7225 (m-10) REVERT: C 273 PHE cc_start: 0.8559 (t80) cc_final: 0.8300 (t80) REVERT: E 161 MET cc_start: 0.3487 (tpp) cc_final: 0.1632 (ttp) REVERT: E 303 MET cc_start: 0.7725 (tmm) cc_final: 0.7439 (tmm) REVERT: E 507 ILE cc_start: 0.7193 (pt) cc_final: 0.6716 (mp) REVERT: G 161 MET cc_start: 0.6410 (pmm) cc_final: 0.6194 (pmm) REVERT: G 202 TYR cc_start: 0.6552 (m-80) cc_final: 0.6307 (m-80) REVERT: G 251 HIS cc_start: 0.7241 (t70) cc_final: 0.6936 (t70) REVERT: G 285 TYR cc_start: 0.8029 (m-80) cc_final: 0.7593 (m-10) REVERT: H 55 GLU cc_start: 0.7459 (tp30) cc_final: 0.7207 (tp30) REVERT: H 187 PHE cc_start: 0.6772 (m-80) cc_final: 0.6551 (m-80) REVERT: H 395 MET cc_start: 0.7546 (mpp) cc_final: 0.6971 (mpp) outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.1845 time to fit residues: 124.8297 Evaluate side-chains 278 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.0980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 30.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 446 ASN F 188 HIS G 207 HIS G 251 HIS ** G 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 69 ASN H 314 GLN M 222 GLN M 251 HIS M 468 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.101005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.081012 restraints weight = 150699.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.082867 restraints weight = 89652.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.084117 restraints weight = 64438.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.084904 restraints weight = 52102.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.085434 restraints weight = 45386.312| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33142 Z= 0.153 Angle : 0.658 9.740 45376 Z= 0.345 Chirality : 0.044 0.190 4984 Planarity : 0.005 0.066 5238 Dihedral : 15.708 177.898 5580 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.87 % Favored : 94.79 % Rotamer: Outliers : 0.88 % Allowed : 7.29 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.14), residues: 3532 helix: 0.60 (0.15), residues: 1184 sheet: -0.79 (0.20), residues: 628 loop : -1.15 (0.14), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 362 TYR 0.019 0.001 TYR A 392 PHE 0.041 0.002 PHE H 273 TRP 0.031 0.002 TRP B 370 HIS 0.004 0.001 HIS G 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (33142) covalent geometry : angle 0.65813 / 0.34 (45376) hydrogen bonds : bond 0.06134 / 4.15 ( 1079) hydrogen bonds : angle 5.75993 / 4.07 ( 2908) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 327 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 MET cc_start: 0.4079 (tpp) cc_final: 0.3876 (tpt) REVERT: A 383 TYR cc_start: 0.7684 (t80) cc_final: 0.7235 (t80) REVERT: B 397 TYR cc_start: 0.8317 (m-80) cc_final: 0.7905 (m-80) REVERT: C 89 LYS cc_start: 0.8070 (mmtm) cc_final: 0.7332 (pttm) REVERT: C 193 MET cc_start: 0.4609 (mtm) cc_final: 0.3681 (mtm) REVERT: C 217 PHE cc_start: 0.7572 (m-80) cc_final: 0.7311 (m-10) REVERT: F 261 CYS cc_start: 0.8517 (t) cc_final: 0.8297 (t) REVERT: F 274 GLU cc_start: 0.9249 (pt0) cc_final: 0.8249 (tm-30) REVERT: G 78 PHE cc_start: 0.7036 (t80) cc_final: 0.6753 (t80) REVERT: G 79 GLU cc_start: 0.7881 (mp0) cc_final: 0.7680 (mp0) REVERT: G 85 LYS cc_start: 0.8684 (mtpp) cc_final: 0.8447 (mtpp) REVERT: G 243 ARG cc_start: 0.8066 (mmm160) cc_final: 0.7541 (mmp80) REVERT: G 285 TYR cc_start: 0.8158 (m-80) cc_final: 0.7798 (m-10) REVERT: H 133 GLU cc_start: 0.8084 (pp20) cc_final: 0.7867 (mm-30) REVERT: H 139 LYS cc_start: 0.7312 (tptp) cc_final: 0.6905 (tppp) REVERT: M 74 MET cc_start: 0.5287 (tpt) cc_final: 0.5083 (tpt) REVERT: M 82 PHE cc_start: 0.6597 (m-80) cc_final: 0.6248 (m-80) REVERT: M 86 TRP cc_start: 0.7722 (t60) cc_final: 0.6573 (t60) outliers start: 28 outliers final: 23 residues processed: 339 average time/residue: 0.1867 time to fit residues: 105.9235 Evaluate side-chains 323 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 300 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 422 THR Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 192 TRP Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain M residue 271 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 354 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 214 optimal weight: 5.9990 chunk 358 optimal weight: 20.0000 chunk 308 optimal weight: 40.0000 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 9.9990 chunk 197 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 238 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 293 ASN ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 ASN C 87 GLN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 GLN ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 267 GLN F 270 ASN F 314 GLN F 358 HIS ** F 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 HIS ** M 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 409 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.096970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.077322 restraints weight = 151975.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.079053 restraints weight = 92350.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.080195 restraints weight = 67439.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.080932 restraints weight = 55204.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.081319 restraints weight = 48541.967| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.124 33142 Z= 0.238 Angle : 0.702 9.247 45376 Z= 0.367 Chirality : 0.045 0.275 4984 Planarity : 0.006 0.061 5238 Dihedral : 15.796 172.642 5580 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.35 % Favored : 94.31 % Rotamer: Outliers : 1.88 % Allowed : 10.04 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.14), residues: 3532 helix: 0.36 (0.15), residues: 1218 sheet: -1.22 (0.20), residues: 608 loop : -1.21 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 209 TYR 0.027 0.002 TYR M 6 PHE 0.041 0.002 PHE C 273 TRP 0.030 0.002 TRP B 370 HIS 0.007 0.002 HIS E 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.24 (33142) covalent geometry : angle 0.70199 / 0.37 (45376) hydrogen bonds : bond 0.05955 / 4.03 ( 1079) hydrogen bonds : angle 5.55175 / 3.91 ( 2908) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 306 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.7493 (t0) cc_final: 0.6966 (m-30) REVERT: A 383 TYR cc_start: 0.7622 (t80) cc_final: 0.7161 (t80) REVERT: B 19 LYS cc_start: 0.8839 (mptt) cc_final: 0.8448 (mppt) REVERT: B 72 ARG cc_start: 0.7396 (mtt90) cc_final: 0.6563 (ptp90) REVERT: B 79 GLU cc_start: 0.7326 (pm20) cc_final: 0.7046 (pm20) REVERT: B 397 TYR cc_start: 0.8185 (m-80) cc_final: 0.7822 (m-80) REVERT: C 37 LEU cc_start: 0.8622 (mt) cc_final: 0.8222 (mt) REVERT: C 89 LYS cc_start: 0.8210 (mmtm) cc_final: 0.7335 (pttm) REVERT: C 193 MET cc_start: 0.5034 (mtm) cc_final: 0.4149 (mtm) REVERT: C 217 PHE cc_start: 0.7535 (m-80) cc_final: 0.7328 (m-10) REVERT: E 491 THR cc_start: 0.6641 (p) cc_final: 0.6264 (t) REVERT: F 261 CYS cc_start: 0.8712 (t) cc_final: 0.8460 (t) REVERT: F 293 TYR cc_start: 0.6784 (m-80) cc_final: 0.6576 (m-80) REVERT: G 85 LYS cc_start: 0.9101 (mtpp) cc_final: 0.8862 (mtpp) REVERT: G 243 ARG cc_start: 0.8242 (mmm160) cc_final: 0.7905 (mmp80) REVERT: G 382 ASN cc_start: 0.8192 (t0) cc_final: 0.7975 (t0) REVERT: H 133 GLU cc_start: 0.8155 (pp20) cc_final: 0.7923 (mm-30) REVERT: H 139 LYS cc_start: 0.7433 (tptp) cc_final: 0.7117 (tptp) REVERT: M 74 MET cc_start: 0.6051 (tpt) cc_final: 0.5767 (tpt) REVERT: M 82 PHE cc_start: 0.6690 (m-80) cc_final: 0.6281 (m-80) outliers start: 60 outliers final: 48 residues processed: 342 average time/residue: 0.1761 time to fit residues: 101.1319 Evaluate side-chains 318 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 270 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 422 THR Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain G residue 20 CYS Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain G residue 391 THR Chi-restraints excluded: chain G residue 455 VAL Chi-restraints excluded: chain G residue 478 VAL Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 192 TRP Chi-restraints excluded: chain H residue 401 VAL Chi-restraints excluded: chain H residue 414 VAL Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 470 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 221 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 165 optimal weight: 6.9990 chunk 251 optimal weight: 9.9990 chunk 286 optimal weight: 10.0000 chunk 357 optimal weight: 9.9990 chunk 191 optimal weight: 7.9990 chunk 330 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 280 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 251 HIS ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 HIS ** F 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 360 HIS ** H 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 HIS ** M 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.096953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.077118 restraints weight = 151602.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.078921 restraints weight = 90972.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.080115 restraints weight = 65972.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.080869 restraints weight = 53735.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.081345 restraints weight = 47141.585| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 33142 Z= 0.183 Angle : 0.649 9.126 45376 Z= 0.338 Chirality : 0.043 0.208 4984 Planarity : 0.005 0.063 5238 Dihedral : 15.805 174.010 5580 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.29 % Favored : 94.37 % Rotamer: Outliers : 1.63 % Allowed : 12.33 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.14), residues: 3532 helix: 0.50 (0.15), residues: 1212 sheet: -1.17 (0.20), residues: 624 loop : -1.27 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 362 TYR 0.017 0.001 TYR C 154 PHE 0.021 0.002 PHE C 273 TRP 0.018 0.002 TRP B 370 HIS 0.006 0.001 HIS E 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (33142) covalent geometry : angle 0.64925 / 0.34 (45376) hydrogen bonds : bond 0.05151 / 3.44 ( 1079) hydrogen bonds : angle 5.40229 / 3.80 ( 2908) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 303 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.7495 (t0) cc_final: 0.6996 (m-30) REVERT: A 383 TYR cc_start: 0.7672 (t80) cc_final: 0.7222 (t80) REVERT: B 72 ARG cc_start: 0.7300 (mtt90) cc_final: 0.6747 (ptp90) REVERT: B 79 GLU cc_start: 0.7298 (pm20) cc_final: 0.6987 (pm20) REVERT: B 397 TYR cc_start: 0.8291 (m-80) cc_final: 0.7903 (m-80) REVERT: C 37 LEU cc_start: 0.8576 (mt) cc_final: 0.8292 (mt) REVERT: C 89 LYS cc_start: 0.8193 (mmtm) cc_final: 0.7322 (pttm) REVERT: C 193 MET cc_start: 0.5089 (mtm) cc_final: 0.4238 (mtm) REVERT: C 217 PHE cc_start: 0.7541 (m-80) cc_final: 0.7309 (m-10) REVERT: C 223 PHE cc_start: 0.5549 (m-80) cc_final: 0.5235 (m-80) REVERT: C 305 PHE cc_start: 0.6106 (OUTLIER) cc_final: 0.5684 (m-80) REVERT: C 336 MET cc_start: 0.7689 (mpp) cc_final: 0.7294 (mpp) REVERT: E 422 THR cc_start: 0.7782 (OUTLIER) cc_final: 0.7546 (t) REVERT: E 491 THR cc_start: 0.6552 (p) cc_final: 0.6287 (t) REVERT: F 89 LYS cc_start: 0.8747 (mppt) cc_final: 0.8375 (mtpt) REVERT: F 261 CYS cc_start: 0.8779 (t) cc_final: 0.8498 (t) REVERT: G 85 LYS cc_start: 0.9058 (mtpp) cc_final: 0.8836 (mtpp) REVERT: G 210 PHE cc_start: 0.8661 (t80) cc_final: 0.8383 (t80) REVERT: G 243 ARG cc_start: 0.8291 (mmm160) cc_final: 0.8035 (mmp80) REVERT: G 359 ILE cc_start: 0.8568 (mp) cc_final: 0.8126 (pt) REVERT: H 139 LYS cc_start: 0.7458 (tptp) cc_final: 0.7153 (tptp) REVERT: M 74 MET cc_start: 0.6125 (tpt) cc_final: 0.5881 (tpt) REVERT: M 82 PHE cc_start: 0.6875 (m-80) cc_final: 0.6560 (m-80) REVERT: M 435 MET cc_start: 0.4455 (ptt) cc_final: 0.3642 (ptm) outliers start: 52 outliers final: 42 residues processed: 335 average time/residue: 0.1802 time to fit residues: 100.9910 Evaluate side-chains 318 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 274 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 422 THR Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain G residue 391 THR Chi-restraints excluded: chain G residue 484 ASP Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 192 TRP Chi-restraints excluded: chain H residue 401 VAL Chi-restraints excluded: chain H residue 414 VAL Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 406 LEU Chi-restraints excluded: chain M residue 470 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 74 optimal weight: 2.9990 chunk 242 optimal weight: 6.9990 chunk 77 optimal weight: 0.1980 chunk 100 optimal weight: 7.9990 chunk 323 optimal weight: 1.9990 chunk 326 optimal weight: 6.9990 chunk 201 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 12 optimal weight: 0.0970 chunk 109 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 251 HIS B 293 ASN ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 HIS ** H 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.097761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.078201 restraints weight = 152011.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.079993 restraints weight = 91069.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.081170 restraints weight = 66120.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.081938 restraints weight = 53939.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.082288 restraints weight = 47276.532| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33142 Z= 0.133 Angle : 0.607 10.649 45376 Z= 0.314 Chirality : 0.042 0.196 4984 Planarity : 0.005 0.106 5238 Dihedral : 15.726 172.583 5580 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.95 % Favored : 94.68 % Rotamer: Outliers : 1.94 % Allowed : 13.05 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.14), residues: 3532 helix: 0.70 (0.15), residues: 1212 sheet: -1.13 (0.20), residues: 624 loop : -1.20 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG G 72 TYR 0.016 0.001 TYR C 154 PHE 0.034 0.001 PHE C 273 TRP 0.019 0.001 TRP F 33 HIS 0.004 0.001 HIS G 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (33142) covalent geometry : angle 0.60695 / 0.31 (45376) hydrogen bonds : bond 0.04705 / 3.16 ( 1079) hydrogen bonds : angle 5.20346 / 3.64 ( 2908) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 299 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.7437 (t0) cc_final: 0.6980 (m-30) REVERT: A 194 LEU cc_start: 0.6200 (tt) cc_final: 0.5995 (pp) REVERT: A 383 TYR cc_start: 0.7649 (t80) cc_final: 0.7202 (t80) REVERT: B 4 LEU cc_start: 0.6202 (OUTLIER) cc_final: 0.5990 (pp) REVERT: B 57 LEU cc_start: 0.8057 (tp) cc_final: 0.7691 (tp) REVERT: B 72 ARG cc_start: 0.7159 (mtt90) cc_final: 0.6715 (ptp90) REVERT: B 79 GLU cc_start: 0.7185 (pm20) cc_final: 0.6941 (pm20) REVERT: B 397 TYR cc_start: 0.8292 (m-80) cc_final: 0.7862 (m-80) REVERT: C 37 LEU cc_start: 0.8593 (mt) cc_final: 0.8389 (mt) REVERT: C 89 LYS cc_start: 0.8210 (mmtm) cc_final: 0.7312 (pttm) REVERT: C 193 MET cc_start: 0.5101 (mtm) cc_final: 0.4272 (mtm) REVERT: C 217 PHE cc_start: 0.7531 (m-80) cc_final: 0.7298 (m-10) REVERT: C 223 PHE cc_start: 0.5370 (m-80) cc_final: 0.5091 (m-80) REVERT: C 305 PHE cc_start: 0.6089 (OUTLIER) cc_final: 0.5671 (m-80) REVERT: E 491 THR cc_start: 0.6547 (p) cc_final: 0.6319 (t) REVERT: F 89 LYS cc_start: 0.8857 (mppt) cc_final: 0.8575 (mtpt) REVERT: F 261 CYS cc_start: 0.8797 (t) cc_final: 0.8532 (t) REVERT: G 161 MET cc_start: 0.5996 (pmm) cc_final: 0.5498 (pmm) REVERT: G 210 PHE cc_start: 0.8652 (t80) cc_final: 0.8358 (t80) REVERT: G 258 THR cc_start: 0.8473 (p) cc_final: 0.8260 (p) REVERT: G 359 ILE cc_start: 0.8743 (mp) cc_final: 0.8347 (pt) REVERT: H 139 LYS cc_start: 0.7385 (tptp) cc_final: 0.7115 (tptp) REVERT: H 170 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.7411 (mp) REVERT: M 74 MET cc_start: 0.6315 (tpt) cc_final: 0.6021 (tpt) REVERT: M 82 PHE cc_start: 0.6906 (m-80) cc_final: 0.6598 (m-80) REVERT: M 435 MET cc_start: 0.4688 (ptt) cc_final: 0.4065 (ptm) outliers start: 62 outliers final: 43 residues processed: 340 average time/residue: 0.1947 time to fit residues: 111.6309 Evaluate side-chains 324 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 278 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain G residue 391 THR Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 192 TRP Chi-restraints excluded: chain H residue 401 VAL Chi-restraints excluded: chain H residue 414 VAL Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain M residue 344 GLN Chi-restraints excluded: chain M residue 406 LEU Chi-restraints excluded: chain M residue 470 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 279 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 284 optimal weight: 10.0000 chunk 298 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 191 optimal weight: 4.9990 chunk 256 optimal weight: 0.0980 chunk 9 optimal weight: 10.0000 chunk 167 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 193 optimal weight: 7.9990 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS C 69 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 GLN ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 HIS ** H 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 HIS ** M 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.094891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.075504 restraints weight = 153301.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.077168 restraints weight = 93592.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.078279 restraints weight = 68732.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.078997 restraints weight = 56394.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.079436 restraints weight = 49683.542| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 33142 Z= 0.229 Angle : 0.696 9.061 45376 Z= 0.361 Chirality : 0.044 0.197 4984 Planarity : 0.005 0.097 5238 Dihedral : 15.808 171.312 5580 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.06 % Favored : 93.60 % Rotamer: Outliers : 2.82 % Allowed : 13.80 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.14), residues: 3532 helix: 0.43 (0.15), residues: 1216 sheet: -1.26 (0.21), residues: 584 loop : -1.26 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 225 TYR 0.018 0.002 TYR M 506 PHE 0.027 0.002 PHE E 210 TRP 0.050 0.002 TRP B 86 HIS 0.007 0.002 HIS M 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.23 (33142) covalent geometry : angle 0.69599 / 0.36 (45376) hydrogen bonds : bond 0.05223 / 3.47 ( 1079) hydrogen bonds : angle 5.40140 / 3.78 ( 2908) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 274 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 LEU cc_start: 0.6078 (tt) cc_final: 0.5846 (pp) REVERT: A 383 TYR cc_start: 0.7654 (t80) cc_final: 0.7186 (t80) REVERT: B 4 LEU cc_start: 0.6143 (OUTLIER) cc_final: 0.5941 (pp) REVERT: B 72 ARG cc_start: 0.7067 (mtt90) cc_final: 0.6560 (ptp90) REVERT: B 79 GLU cc_start: 0.7301 (pm20) cc_final: 0.6856 (pm20) REVERT: B 397 TYR cc_start: 0.8319 (m-80) cc_final: 0.7883 (m-80) REVERT: C 37 LEU cc_start: 0.8646 (mt) cc_final: 0.8324 (mt) REVERT: C 89 LYS cc_start: 0.8365 (mmtm) cc_final: 0.7548 (pttm) REVERT: C 193 MET cc_start: 0.4946 (mtm) cc_final: 0.4105 (mtm) REVERT: C 217 PHE cc_start: 0.7625 (m-80) cc_final: 0.7315 (m-10) REVERT: C 305 PHE cc_start: 0.6291 (OUTLIER) cc_final: 0.5708 (m-80) REVERT: C 336 MET cc_start: 0.7278 (mpp) cc_final: 0.6695 (mpp) REVERT: E 359 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8505 (mp) REVERT: E 422 THR cc_start: 0.7767 (OUTLIER) cc_final: 0.7531 (t) REVERT: F 89 LYS cc_start: 0.8779 (mppt) cc_final: 0.8367 (mtpt) REVERT: F 258 ASN cc_start: 0.8253 (OUTLIER) cc_final: 0.7650 (p0) REVERT: F 261 CYS cc_start: 0.8784 (t) cc_final: 0.8538 (t) REVERT: G 210 PHE cc_start: 0.8690 (t80) cc_final: 0.8280 (t80) REVERT: G 359 ILE cc_start: 0.8830 (mp) cc_final: 0.8423 (pt) REVERT: H 139 LYS cc_start: 0.7609 (tptp) cc_final: 0.7329 (tptp) REVERT: M 74 MET cc_start: 0.6663 (tpt) cc_final: 0.5753 (tpp) REVERT: M 405 ILE cc_start: 0.7792 (tt) cc_final: 0.7506 (tp) outliers start: 90 outliers final: 64 residues processed: 343 average time/residue: 0.1823 time to fit residues: 106.9169 Evaluate side-chains 326 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 257 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain E residue 422 THR Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 258 ASN Chi-restraints excluded: chain G residue 20 CYS Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain G residue 348 GLU Chi-restraints excluded: chain G residue 391 THR Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain G residue 478 VAL Chi-restraints excluded: chain G residue 484 ASP Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 192 TRP Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 401 VAL Chi-restraints excluded: chain H residue 414 VAL Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 406 LEU Chi-restraints excluded: chain M residue 459 ILE Chi-restraints excluded: chain M residue 470 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 186 optimal weight: 10.0000 chunk 166 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 chunk 270 optimal weight: 10.0000 chunk 237 optimal weight: 0.1980 chunk 323 optimal weight: 4.9990 chunk 268 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 278 optimal weight: 7.9990 chunk 188 optimal weight: 0.7980 chunk 195 optimal weight: 10.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 HIS ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 GLN ** F 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 HIS H 188 HIS ** H 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.097541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.077834 restraints weight = 152165.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.079614 restraints weight = 92075.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.080782 restraints weight = 67236.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.081539 restraints weight = 55015.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.082030 restraints weight = 48362.856| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33142 Z= 0.124 Angle : 0.635 16.147 45376 Z= 0.323 Chirality : 0.043 0.354 4984 Planarity : 0.005 0.088 5238 Dihedral : 15.726 171.243 5580 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.61 % Favored : 95.05 % Rotamer: Outliers : 2.03 % Allowed : 15.24 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.14), residues: 3532 helix: 0.66 (0.15), residues: 1226 sheet: -1.17 (0.20), residues: 640 loop : -1.16 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 276 TYR 0.021 0.001 TYR E 37 PHE 0.028 0.001 PHE E 210 TRP 0.059 0.002 TRP B 86 HIS 0.008 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (33142) covalent geometry : angle 0.63522 / 0.32 (45376) hydrogen bonds : bond 0.04394 / 2.95 ( 1079) hydrogen bonds : angle 5.17793 / 3.63 ( 2908) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 294 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 MET cc_start: 0.4436 (tpp) cc_final: 0.3575 (tpt) REVERT: A 383 TYR cc_start: 0.7637 (t80) cc_final: 0.7173 (t80) REVERT: B 57 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7059 (mt) REVERT: B 72 ARG cc_start: 0.7149 (mtt90) cc_final: 0.6574 (ptp90) REVERT: B 79 GLU cc_start: 0.6836 (pm20) cc_final: 0.6608 (pm20) REVERT: C 89 LYS cc_start: 0.8285 (mmtm) cc_final: 0.7450 (pttm) REVERT: C 193 MET cc_start: 0.5162 (mtm) cc_final: 0.4342 (mtm) REVERT: C 217 PHE cc_start: 0.7582 (m-80) cc_final: 0.7308 (m-10) REVERT: C 305 PHE cc_start: 0.6115 (OUTLIER) cc_final: 0.5582 (m-80) REVERT: E 422 THR cc_start: 0.7754 (m) cc_final: 0.7549 (t) REVERT: F 89 LYS cc_start: 0.8842 (mppt) cc_final: 0.8566 (mtpt) REVERT: F 261 CYS cc_start: 0.8809 (t) cc_final: 0.8542 (t) REVERT: G 161 MET cc_start: 0.6006 (pmm) cc_final: 0.5574 (pmm) REVERT: G 210 PHE cc_start: 0.8634 (t80) cc_final: 0.8322 (t80) REVERT: G 258 THR cc_start: 0.8342 (p) cc_final: 0.8126 (p) REVERT: G 359 ILE cc_start: 0.8793 (mp) cc_final: 0.8394 (pt) REVERT: H 133 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7476 (mm-30) REVERT: H 139 LYS cc_start: 0.7523 (tptp) cc_final: 0.7288 (tptp) REVERT: H 170 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7386 (mp) REVERT: H 181 PHE cc_start: 0.4018 (p90) cc_final: 0.3646 (p90) REVERT: M 74 MET cc_start: 0.6193 (tpt) cc_final: 0.5595 (tpp) REVERT: M 405 ILE cc_start: 0.7605 (tt) cc_final: 0.7385 (tp) outliers start: 65 outliers final: 49 residues processed: 343 average time/residue: 0.1791 time to fit residues: 103.8511 Evaluate side-chains 327 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 275 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 348 GLU Chi-restraints excluded: chain G residue 391 THR Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 192 TRP Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 401 VAL Chi-restraints excluded: chain H residue 414 VAL Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 344 GLN Chi-restraints excluded: chain M residue 406 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 279 optimal weight: 0.9980 chunk 157 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 242 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 219 optimal weight: 7.9990 chunk 314 optimal weight: 6.9990 chunk 202 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 334 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 HIS ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 HIS C 69 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 HIS F 371 ASN G 59 HIS ** H 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.097727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.078297 restraints weight = 151614.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.080115 restraints weight = 91034.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.081311 restraints weight = 65772.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.082046 restraints weight = 53418.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.082560 restraints weight = 46891.627| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33142 Z= 0.119 Angle : 0.624 12.867 45376 Z= 0.316 Chirality : 0.042 0.205 4984 Planarity : 0.005 0.080 5238 Dihedral : 15.655 171.271 5580 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.12 % Favored : 94.54 % Rotamer: Outliers : 1.72 % Allowed : 16.30 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.14), residues: 3532 helix: 0.77 (0.15), residues: 1212 sheet: -1.12 (0.20), residues: 644 loop : -1.13 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 243 TYR 0.016 0.001 TYR C 154 PHE 0.043 0.001 PHE M 75 TRP 0.038 0.001 TRP B 86 HIS 0.006 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (33142) covalent geometry : angle 0.62394 / 0.32 (45376) hydrogen bonds : bond 0.04275 / 2.89 ( 1079) hydrogen bonds : angle 5.09996 / 3.57 ( 2908) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 291 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 LEU cc_start: 0.6056 (pp) cc_final: 0.5705 (tt) REVERT: A 383 TYR cc_start: 0.7647 (t80) cc_final: 0.7176 (t80) REVERT: B 72 ARG cc_start: 0.7160 (mtt90) cc_final: 0.6631 (ptp90) REVERT: B 79 GLU cc_start: 0.6784 (pm20) cc_final: 0.6554 (pm20) REVERT: C 89 LYS cc_start: 0.8302 (mmtm) cc_final: 0.7473 (pttm) REVERT: C 193 MET cc_start: 0.5043 (mtm) cc_final: 0.4431 (mtm) REVERT: C 217 PHE cc_start: 0.7615 (m-80) cc_final: 0.7404 (m-10) REVERT: C 305 PHE cc_start: 0.6068 (OUTLIER) cc_final: 0.5527 (m-80) REVERT: C 336 MET cc_start: 0.7315 (mpp) cc_final: 0.6912 (mpp) REVERT: E 303 MET cc_start: 0.7724 (tmm) cc_final: 0.7053 (tmm) REVERT: F 89 LYS cc_start: 0.8837 (mppt) cc_final: 0.8565 (mtpt) REVERT: F 261 CYS cc_start: 0.8738 (t) cc_final: 0.8475 (t) REVERT: G 161 MET cc_start: 0.5959 (pmm) cc_final: 0.5486 (pmm) REVERT: G 210 PHE cc_start: 0.8548 (t80) cc_final: 0.8340 (t80) REVERT: G 243 ARG cc_start: 0.8035 (mmp80) cc_final: 0.7814 (mmp80) REVERT: G 258 THR cc_start: 0.8388 (p) cc_final: 0.8176 (p) REVERT: G 279 CYS cc_start: 0.7566 (t) cc_final: 0.7156 (t) REVERT: G 359 ILE cc_start: 0.8758 (mp) cc_final: 0.8390 (pt) REVERT: H 133 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7418 (mm-30) REVERT: H 139 LYS cc_start: 0.7486 (tptp) cc_final: 0.7250 (tptp) REVERT: H 170 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7375 (mp) REVERT: H 181 PHE cc_start: 0.3996 (p90) cc_final: 0.3617 (p90) REVERT: M 74 MET cc_start: 0.6136 (tpt) cc_final: 0.5909 (tpt) outliers start: 55 outliers final: 45 residues processed: 332 average time/residue: 0.1913 time to fit residues: 107.3854 Evaluate side-chains 325 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 278 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain G residue 348 GLU Chi-restraints excluded: chain G residue 391 THR Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 192 TRP Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 401 VAL Chi-restraints excluded: chain H residue 414 VAL Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 344 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 58 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 198 optimal weight: 0.0570 chunk 165 optimal weight: 4.9990 chunk 318 optimal weight: 5.9990 chunk 228 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 248 optimal weight: 8.9990 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 HIS ** H 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 HIS M 329 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.094869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.075271 restraints weight = 153743.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.077029 restraints weight = 92164.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.078181 restraints weight = 67221.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.078937 restraints weight = 54956.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.079376 restraints weight = 48264.869| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 33142 Z= 0.216 Angle : 0.697 11.578 45376 Z= 0.357 Chirality : 0.044 0.295 4984 Planarity : 0.005 0.072 5238 Dihedral : 15.727 170.479 5580 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.09 % Favored : 93.57 % Rotamer: Outliers : 2.03 % Allowed : 16.33 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.14), residues: 3532 helix: 0.63 (0.15), residues: 1212 sheet: -1.34 (0.20), residues: 620 loop : -1.19 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 71 TYR 0.034 0.002 TYR A 221 PHE 0.040 0.002 PHE C 17 TRP 0.040 0.002 TRP B 86 HIS 0.008 0.001 HIS E 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.22 (33142) covalent geometry : angle 0.69673 / 0.36 (45376) hydrogen bonds : bond 0.04841 / 3.22 ( 1079) hydrogen bonds : angle 5.36970 / 3.78 ( 2908) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 271 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 LEU cc_start: 0.5989 (pp) cc_final: 0.5610 (tt) REVERT: A 383 TYR cc_start: 0.7652 (t80) cc_final: 0.7217 (t80) REVERT: B 79 GLU cc_start: 0.7113 (pm20) cc_final: 0.6702 (pm20) REVERT: C 89 LYS cc_start: 0.8415 (mmtm) cc_final: 0.7599 (pttm) REVERT: C 193 MET cc_start: 0.5172 (mtm) cc_final: 0.4272 (mtm) REVERT: C 217 PHE cc_start: 0.7771 (m-80) cc_final: 0.7544 (m-10) REVERT: C 305 PHE cc_start: 0.6199 (OUTLIER) cc_final: 0.5537 (m-80) REVERT: C 336 MET cc_start: 0.7005 (mpp) cc_final: 0.6495 (mpp) REVERT: E 359 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8516 (mp) REVERT: F 89 LYS cc_start: 0.8798 (mppt) cc_final: 0.8410 (mtpt) REVERT: F 261 CYS cc_start: 0.8597 (t) cc_final: 0.8389 (t) REVERT: G 161 MET cc_start: 0.6184 (pmm) cc_final: 0.5711 (pmm) REVERT: G 210 PHE cc_start: 0.8634 (t80) cc_final: 0.8433 (t80) REVERT: G 359 ILE cc_start: 0.8848 (mp) cc_final: 0.8478 (pt) REVERT: H 139 LYS cc_start: 0.7594 (tptp) cc_final: 0.7358 (tptp) REVERT: H 181 PHE cc_start: 0.4140 (p90) cc_final: 0.3763 (p90) REVERT: M 74 MET cc_start: 0.6808 (tpt) cc_final: 0.6175 (tpp) REVERT: M 303 MET cc_start: 0.8428 (tmm) cc_final: 0.7868 (tmm) REVERT: M 435 MET cc_start: 0.4411 (ptt) cc_final: 0.3589 (ptm) outliers start: 65 outliers final: 54 residues processed: 319 average time/residue: 0.1916 time to fit residues: 103.7742 Evaluate side-chains 315 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 259 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 348 GLU Chi-restraints excluded: chain G residue 391 THR Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 401 VAL Chi-restraints excluded: chain H residue 414 VAL Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 344 GLN Chi-restraints excluded: chain M residue 406 LEU Chi-restraints excluded: chain M residue 470 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 297 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 71 optimal weight: 0.0020 chunk 170 optimal weight: 0.0980 chunk 226 optimal weight: 0.9990 chunk 277 optimal weight: 0.6980 chunk 81 optimal weight: 0.0870 chunk 311 optimal weight: 0.9990 chunk 249 optimal weight: 2.9990 chunk 175 optimal weight: 0.5980 overall best weight: 0.2966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 318 ASN B 251 HIS ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 HIS F 234 HIS F 267 GLN G 59 HIS G 454 GLN ** H 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.097592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.077894 restraints weight = 152738.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.079694 restraints weight = 92407.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.080857 restraints weight = 67246.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.081574 restraints weight = 55015.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.082096 restraints weight = 48570.344| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33142 Z= 0.121 Angle : 0.653 12.683 45376 Z= 0.327 Chirality : 0.043 0.308 4984 Planarity : 0.005 0.072 5238 Dihedral : 15.661 172.959 5580 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.73 % Favored : 94.96 % Rotamer: Outliers : 1.60 % Allowed : 16.93 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.14), residues: 3532 helix: 0.82 (0.15), residues: 1210 sheet: -1.11 (0.20), residues: 644 loop : -1.14 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 114 TYR 0.018 0.001 TYR A 233 PHE 0.040 0.001 PHE C 17 TRP 0.040 0.002 TRP B 86 HIS 0.006 0.001 HIS G 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (33142) covalent geometry : angle 0.65333 / 0.33 (45376) hydrogen bonds : bond 0.04145 / 2.79 ( 1079) hydrogen bonds : angle 5.14118 / 3.61 ( 2908) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 291 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 LEU cc_start: 0.6017 (pp) cc_final: 0.5671 (tt) REVERT: A 383 TYR cc_start: 0.7632 (t80) cc_final: 0.7168 (t80) REVERT: B 74 MET cc_start: 0.8260 (tmm) cc_final: 0.7570 (tpt) REVERT: B 75 PHE cc_start: 0.6225 (t80) cc_final: 0.5935 (t80) REVERT: B 79 GLU cc_start: 0.6775 (pm20) cc_final: 0.6507 (pm20) REVERT: C 89 LYS cc_start: 0.8279 (mmtm) cc_final: 0.7521 (pttm) REVERT: C 193 MET cc_start: 0.5102 (mtm) cc_final: 0.4493 (mtm) REVERT: C 217 PHE cc_start: 0.7707 (m-80) cc_final: 0.7477 (m-10) REVERT: C 305 PHE cc_start: 0.6046 (OUTLIER) cc_final: 0.5450 (m-80) REVERT: C 336 MET cc_start: 0.7281 (mpp) cc_final: 0.6823 (mpp) REVERT: E 303 MET cc_start: 0.7728 (tmm) cc_final: 0.7124 (tmm) REVERT: F 89 LYS cc_start: 0.8827 (mppt) cc_final: 0.8538 (mtpt) REVERT: F 261 CYS cc_start: 0.8518 (t) cc_final: 0.8310 (t) REVERT: G 79 GLU cc_start: 0.7725 (mp0) cc_final: 0.7389 (mp0) REVERT: G 131 ASN cc_start: 0.8935 (m-40) cc_final: 0.8679 (m-40) REVERT: G 161 MET cc_start: 0.6135 (pmm) cc_final: 0.5742 (pmm) REVERT: G 210 PHE cc_start: 0.8566 (t80) cc_final: 0.8352 (t80) REVERT: G 258 THR cc_start: 0.8403 (p) cc_final: 0.8187 (p) REVERT: G 359 ILE cc_start: 0.8814 (mp) cc_final: 0.8426 (pt) REVERT: G 435 MET cc_start: 0.5419 (tpt) cc_final: 0.4382 (ttm) REVERT: H 133 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7387 (mm-30) REVERT: H 139 LYS cc_start: 0.7565 (tptp) cc_final: 0.7329 (tptp) REVERT: H 170 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7364 (mp) REVERT: H 181 PHE cc_start: 0.3960 (p90) cc_final: 0.3587 (p90) REVERT: M 74 MET cc_start: 0.5972 (tpt) cc_final: 0.5581 (tpt) REVERT: M 435 MET cc_start: 0.4586 (ptt) cc_final: 0.3816 (ptm) outliers start: 51 outliers final: 45 residues processed: 329 average time/residue: 0.1898 time to fit residues: 106.2711 Evaluate side-chains 327 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 280 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 348 GLU Chi-restraints excluded: chain G residue 391 THR Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 401 VAL Chi-restraints excluded: chain H residue 414 VAL Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 344 GLN Chi-restraints excluded: chain M residue 470 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 65 optimal weight: 9.9990 chunk 170 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 184 optimal weight: 0.9990 chunk 330 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 289 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 chunk 306 optimal weight: 40.0000 chunk 332 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 251 HIS ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 234 HIS G 59 HIS ** H 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.096864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.077431 restraints weight = 153935.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.079177 restraints weight = 93807.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.080353 restraints weight = 68603.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.081073 restraints weight = 55798.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.081565 restraints weight = 49168.642| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 33142 Z= 0.141 Angle : 0.641 11.961 45376 Z= 0.323 Chirality : 0.043 0.300 4984 Planarity : 0.005 0.069 5238 Dihedral : 15.629 172.345 5580 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.18 % Favored : 94.51 % Rotamer: Outliers : 1.66 % Allowed : 16.99 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.14), residues: 3532 helix: 0.82 (0.15), residues: 1212 sheet: -1.15 (0.21), residues: 620 loop : -1.14 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 19 TYR 0.043 0.001 TYR H 285 PHE 0.033 0.001 PHE C 17 TRP 0.065 0.002 TRP B 86 HIS 0.027 0.001 HIS F 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (33142) covalent geometry : angle 0.64136 / 0.32 (45376) hydrogen bonds : bond 0.04206 / 2.82 ( 1079) hydrogen bonds : angle 5.14303 / 3.62 ( 2908) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6890.82 seconds wall clock time: 120 minutes 4.54 seconds (7204.54 seconds total)